eCite Digital Repository

Author: Holland, BR (Associate Professor Barbara Holland)

Number of items: 85

Journal Article
Stark, TL and Liberles, DA and Holland, BR and O'Reilly, MM, Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization, BMC Evolutionary Biology, 17, (38) pp. 1-16. ISSN 1471-2148 (2017) [Refereed Article]
Sumner, JG and Taylor, A and Holland, BR and Jarvis, PD, Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants, Journal of Mathematical Biology, 75, (6-7) pp. 1619-1654. ISSN 0303-6812 (2017) [Refereed Article] 
Steane, DA and Potts, BM and McLean, EH and Collins, L and Holland, BR and Prober, SM and Stock, WD and Vaillancourt, RE and Byrne, M, Genomic scans across three eucalypts suggest that adaptation to aridity is a genome-wide phenomenon, Genome Biology and Evolution, 9, (2) pp. 253-265. ISSN 1759-6653 (2017) [Refereed Article]
Worth, JRP and Holland, BR and Beeton, NJ and Schonfeld, B and Rossetto, M and Vaillancourt, RE and Jordan, GJ, Habitat type and dispersal mode underlie the capacity for plant migration across an intermittent seaway, Annuals of Botany, 120, (4) pp. 539-549. ISSN 0305-7364 (2017) [Refereed Article]
Halliwell, B and Uller, T and Holland, BR and While, GM, Live bearing promotes the evolution of sociality in reptiles, Nature Communications, 8 Article 2030. ISSN 2041-1723 (2017) [Refereed Article]
Serdoz, S and Egri-Nagy, A and Sumner, J and Holland, BR and Jarvis, PD and Tanaka, MM and Francis, AR, Maximum likelihood estimates of pairwise rearrangement distances, Journal of Theoretical Biology, 423 pp. 31-40. ISSN 0022-5193 (2017) [Refereed Article]
Manning, EM and Holland, BR and Ellingsen, SP and Breen, SL and Chen, X and Humphries, M, Comparison of three statistical classification techniques for maser identification, Publications of the Astronomical Society of Australia, 33 Article e015. ISSN 1448-6083 (2016) [Refereed Article] 
Bruniche-Olsen, A and Austin, JJ and Jones, ME and Holland, BR and Burridge, CP, Detecting selection on temporal and spatial scales: a genomic time-series assessment of selective responses to devil facial tumor disease, PLoS One, 11, (3) Article e0147875. ISSN 1932-6203 (2016) [Refereed Article]
Humphries, MA and Bruno, R and Lai, FY and Thai, PK and Holland, BR and O'Brien, JW and Ort, C and Mueller, JF, Evaluation of monitoring schemes for wastewater-based epidemiology to identify drug use trends using cocaine, methamphetamine, MDMA and methadone, Environmental Science and Technology, 50, (9) pp. 4760-4768. ISSN 0013-936X (2016) [Refereed Article] 
Schmid, J and Magee, PT and Holland, BR and Zhang, N and Cannon, RD and Magee, BB, Last hope for the doomed? Thoughts on the importance of a parasexual cycle for the yeast Candida albicans, Current Genetics, 62, (1) pp. 81-85. ISSN 0172-8083 (2016) [Refereed Article] 
Woodhams, MD and Lockhart, PJ and Holland, BR, Simulating and summarizing sources of gene tree incongruence, Genome Biology and Evolution, 8, (5) pp. 1299-1315. ISSN 1759-6653 (2016) [Refereed Article] 
Fearnhead, P and Yu, S and Biggs, P and Holland, B and French, N, Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods, The Annals of Applied Statistics, 9, (1) pp. 200-224. ISSN 1932-6157 (2015) [Refereed Article]
Larcombe, MJ and Holland, B and Steane, DA and Jones, RC and Nicolle, D and Vaillancourt, RE and Potts, BM, Patterns of reproductive isolation in Eucalyptus - a phylogenetic perspective, Molecular Biology and Evolution, 32, (7) pp. 1833-1846. ISSN 0737-4038 (2015) [Refereed Article] 
Wasef, S and Wood, R and El Merghani, S and Ikram, S and Curtis, C and Holland, B and Willerslev, E and Millar, CD and Lambert, DM, Radiocarbon dating of Sacred Ibis mummies from ancient Egypt, Journal of Archaeological Science: Reports, 4 pp. 355-361. ISSN 2352-409X (2015) [Refereed Article]
Zhang, N and Magee, BB and Magee, PT and Holland, BR and Rodrigues, E and Holmes, AR and Cannon, RD and Schmid, J, Selective advantages of a parasexual cycle for the yeast Candida albicans, Genetics, 200, (4) pp. 1117-1132. ISSN 1943-2631 (2015) [Refereed Article] 
Sumner, JG and Jarvis, PD and Holland, BR, A tensorial approach to the inversion of group-based phylogenetic models, BMC Evolutionary Biology, 14 Article 236. ISSN 1471-2148 (2014) [Refereed Article]
Harris, RL and Holland, BR and Cameron, EZ and Davies, NW and Nicol, SC, Chemical signals in the echidna: differences between seasons, sexes, individuals and gland types, Journal of Zoology, 293, (3) pp. 171-180. ISSN 0952-8369 (2014) [Refereed Article] 
Baxter, RB and Dobbie, PD and Parker, QA and Casewell, SL and Lodieu, N and Burleigh, MR and Lawrie, KA and Kulebi, B and Koester, D and Holland, BR, Component masses of young, wide, non-magnetic white dwarf binaries in the Sloan Digital Sky Survey Data Release 7, Monthly Notices of the Royal Astronomical Society, 440, (4) pp. 3184-3201. ISSN 0035-8711 (2014) [Refereed Article]
Bruniche-Olsen, A and Jones, ME and Austin, JJ and Burridge, CP and Holland, BR, Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease, Biology Letters, 10, (11) Article 20140619. ISSN 1744-9561 (2014) [Refereed Article] 
Binney, BM and Biggs, PJ and Carter, PE and Holland, BR and French, NP, Quantification of historical livestock importation into New Zealand 1860-1979, New Zealand Veterinary Journal, 62, (6) pp. 309-314. ISSN 0048-0169 (2014) [Refereed Article] 
Mohan, V and Stevenson, M and Marshall, J and Fearnhead, P and Holland, BR and Hotter, G and French, NP, Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand, MicrobiologyOpen, 2, (4) pp. 659-673. ISSN 2045-8827 (2013) [Refereed Article]
Holland, BR and Jarvis, PD and Sumner, JG, Low-parameter phylogenetic inference under the general Markov model, Systematic Biology, 62, (1) pp. 78-92. ISSN 1063-5157 (2013) [Refereed Article] 
Grievink, LS and Penny, D and Holland, BR, Missing data and influential sites: Choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice, Genome Biology and Evolution, 5, (4) pp. 681-687. ISSN 1759-6653 (2013) [Refereed Article]
Woodhams, M and Steane, DA and Jones, RC and Nicolle, D and Moulton, V and Holland, BR, Novel distances for Dollo data, Systematic Biology, 62, (1) pp. 62-77. ISSN 1063-5157 (2013) [Refereed Article] 
Cox, MP and Holland, BR and Wilkins, MC and Schmid, J, Reconstructing past changes in locus-specific recombination rates, BMC Genetics, 14 Article 11. ISSN 1471-2156 (2013) [Refereed Article]
Blanke, A and Greve, C and Wipfler, B and Beutel, R and Holland, BR and Misof, B, The identification of concerted convergence in insect heads corroborates Palaeoptera, Systematic Biology, 62, (2) pp. 250-263. ISSN 1063-5157 (2013) [Refereed Article] 
Holland, BR, The rise of statistical phylogenetics, Australian and New Zealand Journal of Statistics, 55, (3) pp. 205-220. ISSN 1369-1473 (2013) [Refereed Article] 
Yu, S and Fearnhead, P and Holland, BR and Biggs, P and Maiden, M and French, N, Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli, Journal of Molecular Evolution, 74, (5-6) pp. 273-280. ISSN 0022-2844 (2012) [Refereed Article] 
Saurabh, K and Holland, BR and Gibb, GC and Penny, D, Gaps: an elusive source of phylogenetic information, Systematic Biology, 61, (6) pp. 1075-1082. ISSN 1063-5157 (2012) [Refereed Article]
Sumner, JG and Jarvis, PD and Fernandez-Sanchez, J and Kaine, BT and Woodhams, MD and Holland, BR, Is the general time-reversible model bad for molecular phylogenetics?, Systematic Biology, 61, (6) pp. 1069-1074. ISSN 1063-5157 (2012) [Refereed Article]
Eytan, RI and Hastings, PA and Holland, BR and Hellberg, ME, Reconciling molecules and morphology: Molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria), Molecular Phylogenetics and Evolution, 62, (1) pp. 159-173. ISSN 1055-7903 (2012) [Refereed Article]
Johnson, KA and Holland, BR and Heslewood, MM and Crayn, DM, Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data, Molecular Phylogenetics and Evolution, 62, (1) pp. 146-158. ISSN 1055-7903 (2012) [Refereed Article]
Sumner, JG and Holland, BR and Jarvis, PD, The Algebra of the General Markov Model on Phylogenetic Trees and Networks, Bulletin of Mathematical Biology, 74, (4) pp. 858-880. ISSN 1522-9602 (2012) [Refereed Article]
White, WTJ and Holland, BR, Faster exact maximum parsimony search with XMP, Bioinformatics, 27, (10) pp. 1359-1367. ISSN 1367-4803 (2011) [Refereed Article]
McGraughran, A and Stevens, M and Holland, BR, Biogeography of Circum-Antarctic springtails. , Molecular Phylogenetics and Evolution, 57, (1) pp. 48-58. ISSN 1055-7903 (2010) [Refereed Article]
Holland, BR and Spencer, HG and Worthy, TH and Kennedy, M, Identifying Cliques of Convergent Characters: Concerted Evolution in the Cormorants and Shags, Systematic Biology, 59, (4) pp. 433-445. ISSN 1063-5157 (2010) [Refereed Article]
Zhang, N and Cannon, RD and Holland, BR and Patchett, ML and Schmid, J, Impact of Genetic Background on Allele Selection in a Highly Mutable Candida albicans Gene, PNG, PLOS One, 5, (3) EJ ISSN 1932-6203 (2010) [Refereed Article]
Grievink, LS and Penny, D and Hendy, MD and Holland, BR, Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree, Systematic Biology, 59, (3) pp. 288-297. ISSN 1063-5157 (2010) [Refereed Article]
McGaughran, A and Holland, BR, Testing the Effect of Metabolic Rate on DNA Variability at the Intra-Specific Level, PLOS One, 5, (3) EJ ISSN 1932-6203 (2010) [Refereed Article]
de Nooijer, S and Holland, BR and Penny, D, The Emergence of Predators in Early Life: There was No Garden of Eden, PLOS One, 4, (6) EJ ISSN 1932-6203 (2010) [Refereed Article]
Zhang, N and Upritchard, JE and Holland, BR and Fenton, LE and Ferguson, MM and Cannon, RD and Schmid, J, Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes, Infection, Genetics and Evolution, 9, (4) pp. 493-500. ISSN 1567-1348 (2009) [Refereed Article] 
French, NP and Midwinter, A and Holland, BR and Collins-Emerson, J and Pattison, R and Colles, F and Carter, P, Molecular Epidemiology of Campylobacter jejuni Isolates from Wild-Bird Fecal Material in Children's Playgrounds, Applied and Environmental Microbiology, 75, (3) pp. 779-783. ISSN 0099-2240 (2009) [Refereed Article]
Shepherd, LD and Holland, BR and Perrie, LR, Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Aspenium ferns , Molecular Phylogenetics and Evolution, 48, (1) pp. 176-187. ISSN 1055-7903 (2008) [Refereed Article]
Grievink, LS and Penny, D and Hendy, MD and Holland, BR, LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites, BMC Evolutionary Biology, 8, (1) pp. 1-6. ISSN 1471-2148 (2008) [Refereed Article]
Holland, BR and Clarke, AC and Meudt, HM, Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution, Systematic Biology, 57, (3) pp. 347-366. ISSN 1063-5157 (2008) [Refereed Article]
Holland, BR and Benthin, S and Lockhart, PJ and Moulton, V and Huber, KT, Using supernetworks to distinguish hybridization from lineage-sorting, BMC Evolutionary Biology, 8, (1) EJ ISSN 1471-2148 (2008) [Refereed Article]
Holland, BR and Conner, G and Huber, K and Moulton, V, Imputing Supertrees and Supernetworks from Quartets, Systematic Biology, 56, (1) pp. 57-67. ISSN 1063-5157 (2007) [Refereed Article]
Shavit, L and Penny, D and Hendy, MD and Holland, BR, The Problem of Rooting Rapid Radiations, Molecular Biology and Evolution, 24, (11) pp. 2400-2411. ISSN 0737-4038 (2007) [Refereed Article]
White, WT and Hills, SF and Gaddam, R and Holland, BR and Penny, D, Treeness Triangles: Visualising the Loss of Phylogenetic Signal, Molecular Biology and Evolution, 24, (9) pp. 1529-1541. ISSN 0737-4038 (2007) [Refereed Article]
Pierson, MJ and Martinez-Arias, R and Holland, BR and Gemmell, NJ and Hurles, ME and Penny, D, Deciphering Past Human Population Movements in Oceania: Provably Optimal Trees of 127 mtDNA Genomes, Molecular Biology and Evolution, 23, (10) pp. 1966-1975. ISSN 0737-4038 (2006) [Refereed Article]
Auch, AF and Henz, SR and Holland, BR and Goker, M, Genome BLAST distance phylogenies inferred from whole plastic and whole mitochondrion genome sequences, BMC Bioinformatics, 7, (July) pp. 1-16. ISSN 1471-2105 (2006) [Refereed Article]
Holmes, AR and Tsao, S and Ong, SW and Lamping, E and Niimi, K and Monk, BC and Niimi, M and Kaneko, A and Holland, BR and Schmid, J and Cannon, RD, Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2, Molecular Microbiology, 62, (1) pp. 170-186. ISSN 0950-382X (2006) [Refereed Article]
Holland, BR and Jermiin, LS and Moulton, V, Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005: Improved Consensus Network Techniques for Genome-Scale Phylogeny, Molecular Biology and Evolution, 23, (5) pp. 848-855. ISSN 0737-4038 (2006) [Refereed Article]
Dress, A and Holland, BR and Huber, KT and Koolen, JH and Moulton, V and Weyer-Menkhoff, J, Δ additive and Δ ultra-additive maps, Gromov's trees, and the Farris transform, Discrete Applied Mathematics: Combinatorial Operations Research and Computer Science, 146, (1) pp. 51-73. ISSN 0166-218X (2005) [Refereed Article] 
Goremykin, V and Holland, BR and Hirsch-Ernst, KI and Hellwig, FH, Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications, Molecular Biology and Evolution, 22, (9) pp. 1813-1822. ISSN 0737-4038 (2005) [Refereed Article]
Holland, BR and Schmid, J, Selecting representative model micro-organisms, BMC Microbiology, 5, (May) pp. 1-11. ISSN 1471-2105 (2005) [Refereed Article]
Holland, BR and Huber, KT and Penny, D and Moulton, V, The Min/Max Squeeze: Guaranteeing a Minimal Tree for Population Data, Molecular Biology and Evolution, 22, (2) pp. 235-242. ISSN 0737-4038 (2005) [Refereed Article]
Kennedy, M and Holland, BR and Gray, RD and Spencer, HG, Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks, Systematic Biology, 54, (4) pp. 620-633. ISSN 1063-5157 (2005) [Refereed Article]
Schmid, J and Cannon, RD and Holland, BR, A futile act? Thoughts on the reproductive biology of Candida albicans, Mycologist, 18, (4) pp. 158-163. ISSN 0269-915X (2004) [Refereed Article] 
Holland, BR and Huber, KT and Moulton, V and Lockhart, PJ, Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny, Molecular Biology and Evolution, 21, (7) pp. 1459-1461. ISSN 0737-4038 (2004) [Refereed Article]
Strimmer, K and Forslund, K and Holland, BR and Moulton, V, A novel exploratory method for visual recombination detection, Genome Biology, 4, (5) pp. R33. ISSN 1465-6914 (2003) [Refereed Article]
Salemi, M and De Oliveira, T and Courgnaud, V and Moulton, V and Holland, BR and Cassol, S and Switzer, WM and Vandamme, AM, Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses, Journal of Virology, 77, (13) pp. 7202-7213. ISSN 0022-538X (2003) [Refereed Article]
Gardner, PP and Holland, BR and Moulton, V and Hendy, M and Penny, D, Optimal alphabets for an RNA world, Proceedings of the Royal Society of London, 270, (1520) pp. 1177-1182. ISSN 0370-1662 (2003) [Refereed Article]
Holland, BR and Penny, D and Hendy, MD, Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock-A Simulation Study, Systematic Biology, 52, (2) pp. 229-238. ISSN 1063-5157 (2003) [Refereed Article]
Wagele, JW and Holland, BR and Dreyer, H and Hackethal, B, Searching factors causing implausible non-monophyly: ssu rDNA phylogeny of Isopoda Asellota (Crustacea: Peracarida) and faster evolution in marine than in freshwater habitats, Molecular Phylogenetics and Evolution, 28, (3) pp. 536-551. ISSN 1055-7903 (2003) [Refereed Article]
Zhang, N and Harrex, AL and Holland, BR and Fenton, LE and Cannon, RD and Schmid, J, Sixty Alleles of the ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus, Genome Research, 13, (9) pp. 2005-2017. ISSN 1088-9051 (2003) [Refereed Article]
Hendy, MD and Holland, BR, Upper bounds on maximum likelihood for phylogenetic trees, Bioinformatics, 19, (2) pp. ii66-ii72. ISSN 1367-4803 (2003) [Refereed Article]
Lambert, DM and Ritchie, PA and Millar, CD and Holland, BR and Drummond, AJ and Baroni, C, Rates of Evolution in Ancient DNA from Adelie Penguins, Science, 295, (5563) pp. 2270-2273. ISSN 0036-8075 (2002) [Refereed Article]
Holland, BR and Huber, KT and Dress, A and Moulton, V, a Plots: A Tool for Analyzing Phylogenetic Distance Data, Molecular Biology and Evolution, 19, (12) pp. 2051-2059. ISSN 0737-4038 (2002) [Refereed Article]
Chor, B and Hendy, MD and Holland, BR and Penny, D, Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach, Molecular Biology and Evolution, 17, (10) pp. 1529-1541. ISSN 0737-4038 (2000) [Refereed Article]
Chapter in Book
Jarvis, PD and Holland, BR and Sumner, JG, Phylogenetic Invariants and Markov Invariants, Reference Module in Life Sciences, Elsevier, BD Roitberg (ed), Amsterdam, Netherlands, pp. 1-3. ISBN 9780128096338 (2017) [Revised Book Chapter]
French, N and Yu, S and Biggs, P and Holland, B and Fearnhead, P and Binney, B and Fox, A and Grove-White, D and Leigh, JW and Miller, W and Muellner, P and Carter, P, Evolution of Campylobacter Species in New Zealand, Campylobacter Ecology and Evolution, Caister Academic Press, SK Sheppard, G Meric (ed), United Kingdom, pp. 221-240. ISBN 978-1-908230-36-2 (2014) [Research Book Chapter] 
Jarvis, PD and Holland, BR and Sumner, JG, Phylogenetic Invariants, Brenner's Encyclopedia of Genetics, Academic Press Ltd Elsevier Science Ltd, S Maloy, K Hughes (ed), United Kingdom, pp. 321-323. ISBN 978-0-08-096156-9 (2013) [Other Book Chapter]
Penny, D and Hendy, MD and Holland, BR, Phylogenetics: Parsimony, Networks, and Distance Methods, Handbook of Statistical Genetics, John Wiley & Sons, Ltd, DJ Balding, M Bishop and C Cannings (ed), West Sussex, England, pp. 489-532. ISBN 978-0-470-05830-5 (2007) [Revised Book Chapter] 
Review
Holland, BR, Book review - Molecular Evolution: A Statistical Approach, Systematic Biology, 64, (3) pp. 545-546. ISSN 1063-5157 (2015) [Review Single Work]
Holland, BR, Analysis of Phylogenetics and Evolution with R, Systematic Biology, 56, (4) pp. 694-696. (2007) [Review Single Work]
Conference Publication
Humphries, MA and Holland, BR and Reynolds, AR and Bruno, RB, Cognitive models in the extreme, Australian Mathematical Psychology Conference 2016, 10-12 February, 2016, Hobart, Tasmania (2016) [Conference Extract]
Humphries, MA and Holland, BR and Karpievitch, YV and Sumner, JG, To gamma or not to gamma? Testing the fit of rates-across-sites models, Phylomania 2012, 8-9 November 2012, University of Tasmania, Hobart, pp. 7. (2012) [Conference Extract]
Kaur, M and Stewart, DC and Janusz, A and Bowman, JP and Holland, BR and Evans, DE, Assessing barley malt associated microbial diversity using next generation sequencing, 2011 Australian Society for Microbiology Annual Meeting, Hobart, Australia (2011) [Conference Extract] 
Kaur, M and Stewart, DC and Janusz, A and Bowman, JP and Holland, BR and Evans, DE, Tapping into barley malt associated microbial diversity using next generation sequencing, Proceedings of the 15th Australian Barley Technical Symposium, 18-21 September 2011, Adelaide, Australia (2011) [Conference Extract] 
Holland, BR and Schardl, CJ and Schmid, J, Endophyte survival without sex, Proceedings of the 6th International Symposium on Fungal Endophytes of Grasses, 25-28 March 2006, Christchurch, New Zealand, pp. 151-154. (2006) [Refereed Conference Paper]
Holland, BR and Conner, G and Huber, KT and Moulton, V, Imputing Supertrees and Supernetworks from Quartets, Lecture Notes in Bioinformatics: Algorithms in Bioinformatics: 6th International Workshop, WABI 2006, 11-13 September 2006, Zurich, Switzerland, pp. 162. ISBN 978-3-540-39583-6 (2006) [Conference Extract] 
Holland, BR and Moulton, V, Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees, Algorithms in Bioinformatics, 15-20 September 2003, Budapest, Hungary, pp. 165-176. ISBN 3-540-20076-2 (2003) [Refereed Conference Paper]
Chor, B and Hendy, MD and Holland, BR and Penny, D, Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach, RECOMB 2000: Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 8-11 April 2000, Tokyo, Japan, pp. 108-117. ISBN 1-58113-186-0 (2000) [Refereed Conference Paper] 
Thesis
Holland, BR, Evolutionary analyses of large data sets: Trees and beyond (2001) [PhD] 

This list was generated on Fri Dec 15 19:32:56 2017.